PMapper - 3D pharmacophore hashes

Encoding of 3D pharmacophores with hashes. This representation is suitable for fast detection of identical pharmacophores without their explicit alignment. It was adapted for 3D ligand-based pharmacophore modeling which requires only 2D strcutures of known active and inactive compounds.


  1. PMapper - representation of 3D pharmacophores (
  2. The idea is to represent 3D pharmacophore as a complete graph where vertices are pharmacophore features and edges are binned distances between them. All possible quadruplets of features (subgraphs) are considered. For each quadruplet a canonical signature is calculated which encodes topology and stereoconfiguration of a quadruplet. The sorted set of all qudruplets and their counts in a pharmacophore is hashed with MD5 hash to get a 3D pharmacophore hash. Figures below illustrate the procedure, for more details pleases refer our publication.

    Generation of 3D pharmacophore hash

    PMapper scheme

    Determination of quadruplet stereoconfiguration

    PMapper quadruplet system

  3. PSearch - 3D ligand-based pharmacophore modeling (
  4. Automated software to generate 3D pharmacophore models based on data sets of known acrive and inactive compounds which does not reqire explicit alignment.

    Model generation workflow


    Examples of 3D ligand-based pharmacophores and observed PDB poses

    PSearch examples

  5. PharMD - MD pharmacophore modeling (
  6. Software to automatically retrieved pharmacophores from MD trajectores of protein-ligand complexes.

    Pharmacophore retrieval and ligand scoring workflow


How to cite

The paper which describes 3D pharmacophore representation (PMapper) and 3D ligand-based pharmacohore modeling (PSearch) approaches:

Kutlushina, A.; Khakimova, A.; Madzhidov, T.; Polishchuk, P. Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures. Molecules 2018, 23, 3094. -

The paper describing MD pharmacophores:

Polishchuk, P.; Kutlushina, A.; Bashirova, D.; Mokshyna, O.; Madzhidov, T., Virtual Screening Using Pharmacophore Models Retrieved from Molecular Dynamic Simulations. International Journal of Molecular Sciences 2019, 20, 5834. -

© Pavel Polishchuk 2010-2019